gene regulation and metabolism

[...]... applied Other chapters in this book address specific questions of gene regulation and metabolism without explicit mention of the connection between networks and the phenotype One of the challenges, computationally, in understanding gene regulation is finding, capturing, and leveraging the information in better-studied networks It is standard practice to apply conclusions from well-studied proteins to... conflicts between genetic and developmental viewpoints and their attempted resolution in molecular biology In M L Dalla Chiara (ed.), Structures and Norms in Science Dordrecht, The Netherlands: Kluwer Academic Publishers, pp 243–264 de Beer, S G (1971) Homology, an Unsolved Problem London: Oxford University Press Depew, D J., and Weber, B (1996) Darwinism Evolving: Systems Dynamics and the Genealogy of... Academic Press 14 Jeremy Ahouse Gehring, Walter J., and Ruddle, Frank (1998) Master Control Genes in Development and Evolution: The Homeobox Story New Haven, Conn.: Yale University Press (Terry Lectures) Gerhart, John, and Kirschner, Marc W (1997) Cells, Embryos, and Evolution: Toward a Cellular and Developmental Understanding of Phenotypic Variation and Evolutionary Adaptability Oxford: Blackwell Science... vertebrate clades that had flight (pterosaurs, birds, and bats) as distinct from the flying insects It should be clear that comparative work is critical, and fortunately the sequencing projects and advances in transcript and protein profiling make comparative work ever easier And the information that can be gleaned from comparative work (borrowing annotations and candidates justified by hypotheses of homology)... wonderfully more complicated problems of understanding what proteins do, how they interact, and how they are regulated, we will need principled ways to interpret profiling information, generate network hypotheses, and annotate myriad functions In that project, homology plays a useful role both in giving a methodological starting point for generating candidate interactions and in reminding us that inference from... their support during the compilation of this book x Preface Gene Regulation and Metabolism This page intentionally left blank 1 Are the Eyes Homologous? Jeremy C Ahouse Since the 1990s research in developmental genetics has followed the approach of borrowing pathways described in one context and testing to see if the members of a pathway or genetic regulatory circuit can be found in a new context This... Goodwin, B (1996) Form and Transformation: Generative and Relational Principles in Biology Cambridge: Cambridge University Press SUGGESTED READING Carroll, Sean B., Grenier, Jennifer K., and Weatherbee, Scott D (2001) From DNA to Diversity: Molecular Genetics and the Evolution of Animal Design Oxford: Blackwell Science Davidson, Eric H (2001) Genomic Regulatory Systems: Development and Evolution London:... Bolker and Raff, 1997) These include the failure to distinguish between orthology and paralogy,1 the confusion of analogy (convergence) and homology (noting that gene- swapping experiments do not resolve this question), the failure to notice that orthologous genes can be recruited and expressed in structures whose similarities may not be due to common ancestry So, for example, the distal-less gene (the... that are generated when we focus on differences attributed to selection rather than on similarities attributed to homology C J Lowe and G A Wray studied several homeobox genes and concluded that they were recruited into new roles: ‘‘Each of these cases [orthodenticle, distal-less, engrailed expression in brittle stars, sea urchins, and sea stars] represents recruitment (co-option) of a homeobox gene to... profiles and the need to interpret them has encouraged researchers to use known regulatory networks to establish expectations against which profiling experiments can be statistically compared I will offer an operational definition of homology, watch it at work in a current example of gene regulation (eye development), and endorse hypotheses of gene regulatory homology that push experimental work and set . approaches to metabolism and gene regulation. This is an area of computational biology that welcomes new methods, ideas, and approaches with the goal of generating a better understanding of the. questions of gene reg- ulation and metabolism without explicit mention of the connection between networks and the phenotype. One of the challenges, compu- tationally, in understanding gene regulation. Genomics Isaac S. Kohane, Alvin Kho, and Atul J. Butte, 2002 Gene Regulation and Metabolism Postgenomic Computational Approaches edited by Julio Collado-Vides and Ralf Hofesta ¨ dt A Bradford Book The